Identification and characterization of Long non-coding RNAs in primary human monocytes and neutrophils

Abstract

Long non-coding RNAs (LncRNAs) are described as key players in several biological and pathological processes thanks to their ability to regulate gene expression [1]. The role of LncRNAs in development and cancer has been deeply investigated [2]. Conversely, few is known about LncRNAs in immune response [3]. With this background, our study aims to identify and characterize the LncRNAs in human neutrophils (PMN) and monocytes responses to TLR4 activation. RNA seq was performed on human CD14+ monocytes and highly-pure PMN stimulated with LPS for 90min and 4h or left untreated. Differential gene expression was analysed by DESeq2. LPS is able both to induce the de novo expression and to modulate constitutively expressed LncRNAs in monocytes and PMN. Further analysis of the 2278 LncRNAs regulated by LPS in both cell types allowed us to identify: i)626 LncRNAs commonly modulated by LPS in both phagocyte types; ii)1186 LncRNAs modulated uniquely in monocytes, and 466 modulated selectively in PMN. Moreover, K-mean clustering analysis identifies three groups of LncRNAs differently modulated by LPS: Early: LncRNAs modulated by LPS already at 90m; Early and transient: rapidly modulated LncRNAs whose expression returns to the basal level by 4h; Late: LncRNAs modulated by LPS after 4h. Moreover, eRNA and canonical LncRNAs were identified based on H3K4me3 and H3K4me1 ChIP-seq analysis. Finally, to get insight into LncRNAs function, protein coding genes in cis to LncRNAs were analysed for GO Term enrichment. This in silico analysis suggests a likely role for LncRNAs in the regulation of several phagocyte processes, among which the most representative are cytokine production, signal transduction, chromatin organization and metabolic processes. Our study shows that LncRNAs are modulated and are likely involved in the regulation of many biological processes in human PMN and monocytes triggered by TLR4 activation. The detail functional characterization of this class of regulators is under investigation